Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2

Ananya Acharya,Ralf Seidel,Vera Kissling,Raphaël Guérois,Kristina Kasaciunaite,Martin Göse,Petr Cejka

doi:10.1038/s41467-021-26863-y

Abstract

The Dna2 helicase-nuclease functions in concert with the replication protein A (RPA) in DNA double-strand break repair. Using ensemble and single-molecule biochemistry, coupled with structure modeling, we demonstrate that the stimulation of S. cerevisiae Dna2 by RPA is not a simple consequence of Dna2 recruitment to single-stranded DNA. The large RPA subunit Rfa1 alone can promote the Dna2 nuclease activity, and we identified mutations in a helix embedded in the N-terminal domain of Rfa1 that specifically disrupt this capacity. The same RPA mutant is instead fully functional to recruit Dna2 and promote its helicase activity. Furthermore, we found residues located on the outside of the central DNA-binding OB-fold domain Rfa1-A, which are required to promote the Dna2 motor activity. Our experiments thus unexpectedly demonstrate that different domains of Rfa1 regulate Dna2 recruitment, and its nuclease and helicase activities. Consequently, the identified separation-of-function RPA variants are compromised to stimulate Dna2 in the processing of DNA breaks. The results explain phenotypes of replication-proficient but radiation-sensitive RPA mutants and illustrate the unprecedented functional interplay of RPA and Dna2.

Highlights

The Dna[2] helicase-nuclease functions in concert with the replication protein A (RPA) in DNA double-strand break repair
We show that cognate heterotrimeric RPA promoted the nuclease activity of wild type Dna[2] (Fig. 1a–e), and the helicase activity of the nuclease-dead Dna2-E675A, unlike the non-cognate factors (Fig. 1f–h)
Human mitochondrial single-stranded DNA (ssDNA) binding protein, which bears no sequence similarity to RPA, and rather resembles prokaryotic SSB, in contrast inhibited both activities of Dna[2] (Fig. 1d, f–h), the same results were obtained with other Dna[2] concentrations

Summary

Introduction

The Dna[2] helicase-nuclease functions in concert with the replication protein A (RPA) in DNA double-strand break repair. The large RPA subunit Rfa[1] alone can promote the Dna[2] nuclease activity, and we identified mutations in a helix embedded in the N-terminal domain of Rfa[1] that disrupt this capacity. The same RPA mutant is instead fully functional to recruit Dna[2] and promote its helicase activity. Our experiments unexpectedly demonstrate that different domains of Rfa[1] regulate Dna[2] recruitment, and its nuclease and helicase activities. (Rfa1-F) provides only a minor, if any, contribution to DNA binding, and rather mediates specific physical interactions with RPA-binding proteins, along with the C-terminus of Rfa[21,8,9]

Methods

Results

Conclusion